usegalaxy-eu · galaxy-social-bot · Nov 10, 2024 · Nov 10, 2024
diff --git a/posts/feed_bot/galaxy_europe/2024-11-08-galaxy-imaging-fair-pipelines-group1.md b/posts/feed_bot/galaxy_europe/2024-11-08-galaxy-imaging-fair-pipelines-group1.md
@@ -0,0 +1,84 @@
+---
+media:
+- mastodon-eu-freiburg
+- matrix-eu-announce
+- linkedin-galaxyproject
+mentions:
+  mastodon-eu-freiburg:
+  - [email protected]
+hashtags:
+  mastodon-eu-freiburg:
+  - UseGalaxy
+  - GalaxyProject
+  - UniFreiburg
+  - EOSC
+  - EuroScienceGateway
+  linkedin-galaxyproject:
+  - UseGalaxy
+  - GalaxyProject
+  - UniFreiburg
+  - EOSC
+  - EuroScienceGateway
+---
+📝 New blog post Released!
+https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/
+
+The Helmholtz Metadata Conference (HMC) 2024
+--------------------------------------------
+
+The Helmholtz Metadata Collaboration (HMC) focuses on enhancing research
+data quality through metadata, implementing this approach throughout the
+entire organisation. Its primary goal is to make the extensive research
+data produced by Helmholtz Centres findable, accessible, interoperable,
+and reusable (FAIR) for the scientific community. This year’s Helmholtz
+Metadata Conference (HMC) was held virtually in Gather Town from November
+4th to 6th. The event targeted scientists, data professionals, software developers,
+and anyone engaged with metadata. Sessions covered a range of topics,
+including metadata management, ontologies, metadata schemas and formats,
+semantics, standardisation, and workflows.
+
+![HMC_logo.png](https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/HMC_logo.png)
+
+Building FAIR Bioimage Pipelines with Galaxy
+--------------------------------------------
+
+In the “workflow” session, I presented the application of Galaxy to develop
+FAIR analysis pipelines for metadata annotation and image management in
+high\-content screening (HCS) bioimaging. In fact, Galaxy workflows enhance
+data FAIRness by allowing annotation, collaboration, and public sharing.
+Additionally, Galaxy tools are transparent, meaning they can be easily
+inspected within the Galaxy Tool Shed, providing a clear view of their
+structure.
+
+![pipeline_ip.png](https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/pipeline_ip.png)
+
+Integrating OMERO and Galaxy
+----------------------------
+
+During the conference, I discussed integrating OMERO’s upload and image
+annotation features with Galaxy’s image analysis workflows.
+This integration enables images to be automatically enriched with metadata
+(e.g., key\-value pairs, tags, raw data, regions of interest) and uploaded
+to a user\-defined OMERO server using a new OMERO tool suite developed in
+Galaxy. Currently, the suite offers tools for image and ROI uploads,
+metadata enrichment, and data filtering or retrieval, making it simple
+to transfer data and metadata to an OMERO instance.
+
+![img.png](https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/omero_pipeline.png)
+
+Combining Image Processing and Data Management in One Workflow
+--------------------------------------------------------------
+
+Image processing can be added to OMERO workflows. Users can retrieve
+images from a local server and perform image analyses, such as annotation,
+segmentation, or background subtraction. Galaxy is a powerful tool for
+image analysis, integrating popular software like CellProfiler and connecting
+with cloud services like OMERO and the IDR. This integration allows for
+efficient access to and management of image data, which is invaluable in
+bioimaging. Automated pipelines streamline the handling of complex metadata,
+ensuring data integrity and fostering interdisciplinary collaboration.
+This approach not only boosts the efficiency of HCS bioimaging but
+also aligns with the scientific community’s FAIR principles, driving
+scientific discovery and innovation forward.
+
+The presentation was shared on [Zenodo](https://zenodo.org/records/14044640)
diff --git a/posts/feed_bot/galaxy_europe/2024-11-08-galaxy-imaging-fair-pipelines-group2.md b/posts/feed_bot/galaxy_europe/2024-11-08-galaxy-imaging-fair-pipelines-group2.md
@@ -0,0 +1,76 @@
+---
+media:
+- bluesky-galaxyproject
+mentions:
+  bluesky-galaxyproject:
+  - galaxyproject.bsky.social
+hashtags:
+  bluesky-galaxyproject:
+  - UseGalaxy
+  - GalaxyProject
+  - UniFreiburg
+  - EOSC
+  - EuroScienceGateway
+---
+📝 New blog post Released!
+https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/
+
+The Helmholtz Metadata Conference (HMC) 2024
+--------------------------------------------
+
+The Helmholtz Metadata Collaboration (HMC) focuses on enhancing research
+data quality through metadata, implementing this approach throughout the
+entire organisation. Its primary goal is to make the extensive research
+data produced by Helmholtz Centres findable, accessible, interoperable,
+and reusable (FAIR) for the scientific community. This year’s Helmholtz
+Metadata Conference (HMC) was held virtually in Gather Town from November
+4th to 6th. The event targeted scientists, data professionals, software developers,
+and anyone engaged with metadata. Sessions covered a range of topics,
+including metadata management, ontologies, metadata schemas and formats,
+semantics, standardisation, and workflows.
+
+![HMC_logo.png](https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/HMC_logo.png)
+
+Building FAIR Bioimage Pipelines with Galaxy
+--------------------------------------------
+
+In the “workflow” session, I presented the application of Galaxy to develop
+FAIR analysis pipelines for metadata annotation and image management in
+high\-content screening (HCS) bioimaging. In fact, Galaxy workflows enhance
+data FAIRness by allowing annotation, collaboration, and public sharing.
+Additionally, Galaxy tools are transparent, meaning they can be easily
+inspected within the Galaxy Tool Shed, providing a clear view of their
+structure.
+
+![pipeline_ip.png](https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/pipeline_ip.png)
+
+Integrating OMERO and Galaxy
+----------------------------
+
+During the conference, I discussed integrating OMERO’s upload and image
+annotation features with Galaxy’s image analysis workflows.
+This integration enables images to be automatically enriched with metadata
+(e.g., key\-value pairs, tags, raw data, regions of interest) and uploaded
+to a user\-defined OMERO server using a new OMERO tool suite developed in
+Galaxy. Currently, the suite offers tools for image and ROI uploads,
+metadata enrichment, and data filtering or retrieval, making it simple
+to transfer data and metadata to an OMERO instance.
+
+![img.png](https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/omero_pipeline.png)
+
+Combining Image Processing and Data Management in One Workflow
+--------------------------------------------------------------
+
+Image processing can be added to OMERO workflows. Users can retrieve
+images from a local server and perform image analyses, such as annotation,
+segmentation, or background subtraction. Galaxy is a powerful tool for
+image analysis, integrating popular software like CellProfiler and connecting
+with cloud services like OMERO and the IDR. This integration allows for
+efficient access to and management of image data, which is invaluable in
+bioimaging. Automated pipelines streamline the handling of complex metadata,
+ensuring data integrity and fostering interdisciplinary collaboration.
+This approach not only boosts the efficiency of HCS bioimaging but
+also aligns with the scientific community’s FAIR principles, driving
+scientific discovery and innovation forward.
+
+The presentation was shared on [Zenodo](https://zenodo.org/records/14044640)